Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.00 kDa 
• Atom Count: 1309 
• Residue Count: 146 
• Unique protein chains: 1

6TYY

Hedgehog autoprocessing mutant D46H

• DOI: 10.2210/pdb6TYY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-08-09 Released: 2019-11-20 
• Deposition Author(s): Li, H., Li, Z., Wang, C., Callahan, B.P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Literature

General Base Swap Preserves Activity and Expands Substrate Tolerance in Hedgehog Autoprocessing.

Zhao, J., Ciulla, D.A., Xie, J., Wagner, A.G., Castillo, D.A., Zwarycz, A.S., Lin, Z., Beadle, S., Giner, J.L., Li, Z., Li, H., Banavali, N., Callahan, B.P., Wang, C.

(2019) J Am Chem Soc 141: 18380-18384

• PubMed: 31682419 
• DOI: 10.1021/jacs.9b08914
• Primary Citation of Related Structures:  
  6TYY


• PubMed Abstract: 
  

Hedgehog (Hh) autoprocessing converts Hh precursor protein to cholesterylated Hh ligand for downstream signaling. A conserved active-site aspartate residue, D46, plays a key catalytic role in Hh autoprocessing by serving as a general base to activate substrate cholesterol. Here we report that a charge-altering Asp-to-His mutant (D46H) expands native cholesterylation activity and retains active-site conformation. Native activity toward cholesterol was established for D46H in vitro using a continuous FRET-based autoprocessing assay and in cellulo with stable expression in human 293T cells. The catalytic efficiency of cholesterylation with D46H is similar to that with wild type (WT), with k _max / K _M = 2.1 × 10 ³ and 3.7 × 10 ³ M ^-1 s ^-1 , respectively, and an identical p K _a = 5.8 is obtained for both residues by NMR. To our knowledge this is the first example where a general base substitution of an Asp for His preserves both the structure and activity as a general base. Surprisingly, D46H exhibits increased catalytic efficiency toward non-native substrates, especially coprostanol (>200-fold) and epicoprostanol (>300-fold). Expanded substrate tolerance is likely due to stabilization by H46 of the negatively charged tetrahedral intermediate using electrostatic interactions, which are less constrained by geometry than H-bond stabilization by D46. In addition to providing fundamental insights into Hh autoprocessing, our findings have important implications for protein engineering and enzyme design.

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Organizational Affiliation: 

Department of Chemistry , Binghamton University, State University of New York , Binghamton , New York 13902 , United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein hedgehog	A	146	Drosophila melanogaster	Mutation(s): 1  Gene Names: hh, CG4637
Find proteins for Q02936 (Drosophila melanogaster) Explore Q02936  Go to UniProtKB:  Q02936

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.381	α = 90
b = 78.381	β = 90
c = 37.351	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-08-09 
• Released Date: 2019-11-20 
Deposition Author(s): Li, H., Li, Z., Wang, C., Callahan, B.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI140726
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI141178
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA206592

Revision History 

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence, Database references